tbuckley/cabot-search huggingface dataset:
Abstract 2970: Oncometabolites confer vulnerabilities in NAD biosynthesis via NAPRT gene silencing
Authors: Katelyn Noronha, Jiayu Liang, Ranjit Bindra
Journal: Cancer Research (2022)

Abstract Cancer associated mutations in citric acid cycle enzymes cause overproduction of 2-hydroxyglutarate (2HG), fumarate, or succinate, commonly referred to as oncometabolites. These oncometabolite producing mutations are prevalent in 70% of gliomas, &amp;gt;76% of hereditary leiomyomatosis and renal cell carcinoma, and &amp;gt;25% of paraganglioma and pheochromocytomas, respectively. These oncometabolite producing cancers harbor vulnerabilities in multiple cellular pathways because oncometabolites competitively inhibit alpha ketoglutarate dependent dioxygenases. This group of enzymes includes the ten eleven translocation (TET) family of enzymes, which catalyze locus specific DNA demethylation. Thus, oncometabolite producing cancers have been shown to exhibit global DNA hypermethylation, which drastically alters gene expression in the cell and is thought to occur via TET inhibition. Cells with isocitrate dehydrogenase 1 (IDH1) mutations, which produce 2HG, have loss of expression of a critical NAD biosynthesis enzyme, nicotinate phosphoribosyltransferase (NAPRT). We show that in addition to IDH1 mutant cells, fumarate hydratase (FH)-deficient isogenic cell lines, which overproduce fumarate, show loss of NAPRT expression, which can be targeted by nicotinamide phosphoribosyltransferase (NAMPT) inhibitors. The goal of our work is to determine if this NAPRT silencing is present in many oncometabolite producing cancers, elucidate the mechanism of silencing, and test therapies to target this vulnerability in NAD biosynthesis. FH-deficient cancer cell lines show reduction of NAPRT mRNA levels by qRT-PCR and absence of protein by western blot, suggesting a reduction in NAPRT transcription. In addition, FH-deficient cell lines exhibit synthetic lethality in short term cell viability assays when treated with NAMPT inhibitor, FK866, which inhibits a parallel NAD biosynthesis pathway. Cell viability is not rescued by nicotinic acid supplementation in FH-deficient lines while parental lines are rescuable, validating the loss of functional NAPRT in only FH-deficient lines. Furthermore, patient samples of FH-deficient renal cell carcinomas show higher NAPRT promoter methylation compared to healthy tissue via methylation array. Ongoing studies are investigating the role of TET1/2/3 enzymes in NAPRT promoter methylation. Together, these results suggest that hypermethylation of the NAPRT promoter is associated with silencing of NAPRT expression in FH-deficient cancers, which can be therapeutically targeted through NAMPT inhibition. Citation Format: Katelyn Noronha, Jiayu Liang, Ranjit Bindra. Oncometabolites confer vulnerabilities in NAD biosynthesis via NAPRT gene silencing [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2022; 2022 Apr 8-13. Philadelphia (PA): AACR; Cancer Res 2022;82(12_Suppl):Abstract nr 2970.
Abstract 2456: Mass spectrometry imaging reveals distinct differences in glycogen accumulation in lung tumors from Appalachian patients
Authors: Michael D. Buoncristiani, Lindsey R. Conroy, Harrison Clarke, Lyndsay E. Young, Ramon C. Sun
Journal: Cancer Research (2022)

Abstract Lung cancer is the leading cause of cancer related death in the United States, with patients from rural Appalachia having drastically higher incidence and mortality rates, driven by largely unknown mechanisms. Identifying molecular features that contribute to this health disparity is a critical step in lung cancer research that could lead to predictive biomarkers and personalized therapy for the Appalachia population. Recently, aberrant glycogen accumulation in lung tumors has been reported to promote lung cancer progression. However, the full clinical implications of dysregulated glycogen metabolism and its role in lung cancer health disparities has yet to be explored. Matrix-assisted laser desorption/ionization-mass spectrometry imaging (MALDI-MSI) is a new and innovative technique that combines mass spectrometry with high resolution imaging, enabling the detection of hundreds of analytes with spatial distribution. We recently developed an advanced method to analyze glycogen content in formalin-fixed paraffin-embedded tissues using MALDI-MSI. With this technique, we analyzed glycogen chain length and glycogen phosphate content from tissue microarrays containing over 100 lung cancer patient samples banked at the University of Kentucky. Our patient cohort included adenocarcinoma and squamous cell carcinoma patients from Appalachian and non-Appalachian counties, with diverse cytopathological features. We found significant glycogen accumulation and higher glycogen phosphate content in lung tumor tissue compared to match normal lung across all patients. Further, we found glycogen accumulation is markedly high in adenocarcinoma patients compared to other lung cancer subtypes. Interestingly, Appalachian adenocarcinoma patients exhibit increased glycogen accumulation and higher glycogen phosphate content than patients from non-Appalachian counties. These data suggest differential glycogen accumulation is a unique feature of lung tumors from Appalachian adenocarcinoma patients. Our study highlights the potential clinical applications of MALDI-MSI for digital pathology, biomarker applications, and reveals molecular features that contribute to the health disparity in Appalachian lung cancer patients that warrant further molecular analysis. Citation Format: Michael D. Buoncristiani, Lindsey R. Conroy, Harrison Clarke, Lyndsay E. Young, Ramon C. Sun. Mass spectrometry imaging reveals distinct differences in glycogen accumulation in lung tumors from Appalachian patients [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2022; 2022 Apr 8-13. Philadelphia (PA): AACR; Cancer Res 2022;82(12_Suppl):Abstract nr 2456.
A single-cell map of dynamic chromatin landscapes of immune cells in renal cell carcinoma
Authors: Nikos Kourtis, Qingqing Wang, Bei Wang, Erin Oswald, Christina Adler, Samvitha Cherravuru, Evangelia Malahias, Lance Zhang, Jacquelynn Golubov, Qiaozhi Wei, Samantha Lemus, Min Ni, Yueming Ding, Yi Wei, Gurinder S. Atwal, Gavin Thurston, Lynn E. Macdonald, Andrew J. Murphy, Ankur Dhanik, Matthew A. Sleeman, Scott S. Tykodi, Dimitris Skokos
Journal: Nature Cancer (2022)

Abstract A complete chart of the chromatin regulatory elements of immune cells in patients with cancer and their dynamic behavior is necessary to understand the developmental fates and guide therapeutic strategies. Here, we map the single-cell chromatin landscape of immune cells from blood, normal tumor-adjacent kidney tissue and malignant tissue from patients with early-stage clear cell renal cell carcinoma (ccRCC). We catalog the T cell states dictated by tissue-specific and developmental-stage-specific chromatin accessibility patterns, infer key chromatin regulators and observe rewiring of regulatory networks in the progression to dysfunction in CD8 + T cells. Unexpectedly, among the transcription factors orchestrating the path to dysfunction, NF-κB is associated with a pro-apoptotic program in late stages of dysfunction in tumor-infiltrating CD8 + T cells. Importantly, this epigenomic profiling stratified ccRCC patients based on a NF-κB-driven pro-apoptotic signature. This study provides a rich resource for understanding the functional states and regulatory dynamics of immune cells in ccRCC.
Abstract 2843: Development of a translatable CD19 CAR-T platform for drug discovery
Authors: Lauren Kelsey, Jezrom Self-Fordham, Eva Oswald, Ilona Aylott, Daniel Rocca, Robert Nunan, David Harris, Julia Schueler, Rhiannon Jenkinson
Journal: Cancer Research (2022)

Abstract Chimeric Antigen Receptor (CAR)-T cell therapy has achieved great success with specificity, efficacy, safety and ingenuity. CAR cell technology is advancing rapidly, with ever increasing capabilities for cancer treatment both with regard to tumor types and the CAR cell used (NK, Macrophage, T). To date, the most successful application remains the treatment of B cell lymphoma using CD19-specific CAR-T cells. Here we describe how to efficiently generate and expand a CD19 CAR-T cell and validate their efficacy in in-vitro and in-vivo studies. HLA-A*02:01+ CD3+ T-cells were transduced to express a clinically tested CD19-specific CAR to &amp;gt;80% efficiency and reproducibly expanded to &amp;gt;68 fold over a 19-day period. After sufficient expansion, cells were validated in in-vitro studies to assess their efficacy, utilizing a HLA-A*02:01+ patient derived xenograft (PDX) CD19+ cell line, alongside human cancer cell lines RAJI (CD19+) and K562 (CD19-). Flow cytometry analysis revealed the potent ability of CD19-CAR-T cells to kill CD19+ targets in a dose-dependent fashion. Highly specific killing at all E:T ratios was observed, with negligible off target killing identified. Supportive supernatant analysis showed highly elevated pro-inflammatory cytokine concentrations, identifying enhanced activation of CAR-T cells in the presence of CD19+ target cells only. After successful in-vitro batch testing for on-target killing CAR-T cells were released for in-vivo survival studies. Mice were inoculated with the same strains of CD19+ cells used during in-vitro validation to produce a tumor burdened model. CAR-T cells or non-transduced cells from the same donor were transfused and survival rates, tumor progression and tolerability assessments were observed over several weeks. Ex-vivo tissue and sera analysis further characterized these highly efficacious human CAR-T cells. These assays represent the capability to produce, expand and study CAR-effector cells both in-vitro and in-vivo. Careful consideration of human target cells enables the efficient translation of in-vitro efficacy data to whole organism mouse models. Citation Format: Lauren Kelsey, Jezrom Self-Fordham, Eva Oswald, Ilona Aylott, Daniel Rocca, Robert Nunan, David Harris, Julia Schueler, Rhiannon Jenkinson. Development of a translatable CD19 CAR-T platform for drug discovery [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2022; 2022 Apr 8-13. Philadelphia (PA): AACR; Cancer Res 2022;82(12_Suppl):Abstract nr 2843.
Abstract 5326: Targeted extracellular vesicle to deliver combined chemotherapies to treat cancers
Authors: Kai Chen, Yingnan Si, Seulhee Kim, Zhuoxin Zhou, Lufang Zhou, X. Margaret Liu
Journal: Cancer Research (2022)

Abstract Extracellular vesicles (EV), facilitated with cancer-targeted antibody or peptide, have been demonstrated as an effective delivery vehicle of chemotherapy and gene therapy. This study aimed to develop and evaluate a targeted EV to deliver a newly identified natural cytotoxic marine compound verrucarin A (Ver-A) or combination with highly potent microtubule polymerization inhibitor mertansine (DM1). The tumor models, glioblastoma (GBM), triple-negative breast cancer (TNBC) and others, were used to validate the developed targeted therapy. First, the stirred-tank bioreactor-based EV biomanufacturing was optimized by developing a two-step purification procedure using size exclusion (300 kDa) and affinity (CD63) columns in liquid chromatography system. Second, both single and dual tumor-targeting monoclonal antibodies (mAbs), such as anti-SSTR2, CD276, EGFR and/or CD47 mAb either developed in house or used in clinics, were tagged on the surface of PEGylated EV to construct mAb-EV-drugs. The flow cytometry analysis, live-cell confocal images and IC50 assay revealed the effective surface binding, intracellular drug delivery and high anti-cancer cytotoxicity of mAb-EV-drugs in cancer cell lines, and the biodistribution study confirmed the tumor targeting in xenograft mouse models. Furthermore, the maximum tolerated dose study showed minimal systemic toxicity, as confirmed by hematoxylin and eosin staining of multiple important organs. Finally, the anti-tumor efficacy study demonstrated significant inhibition of tumor growth by mAb-EV-Ver-A or Ver-A/DM1 in cell line-derived xenograft models, patient-derived xenograft models, and/or immunocompetent xenograft models. This study suggested that the targeted EV is an efficient platform to deliver combined potent chemotherapies to treat cancer or tumor. Citation Format: Kai Chen, Yingnan Si, Seulhee Kim, Zhuoxin Zhou, Lufang Zhou, X. Margaret Liu. Targeted extracellular vesicle to deliver combined chemotherapies to treat cancers [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2022; 2022 Apr 8-13. Philadelphia (PA): AACR; Cancer Res 2022;82(12_Suppl):Abstract nr 5326.
Abstract 2192: HSF1 downregulation of CCL5 reduces CD8 + T cell trafficking in breast cancer
Authors: Curteisha LeeAnn Jacobs, Sakhi Shan, Wen-Cheng Lu, Richard Carpenter
Journal: Cancer Research (2022)

Abstract Breast cancer is the second leading cause of cancer-related death in women. The presence of cytotoxic immune cells, specifically CD8+ T cells, in breast tumors is associated with better patient outcomes. Understanding the mechanisms that regulate the infiltration of CD8+ T cells into breast tumors could improve the treatment and enhance patient overall survival. Utilizing a novel HSF1 activity gene signature, we observed that HSF1 activity was negatively associated with the presence of CD8+ T cells in breast cancer patients. Both CIBERSORT analysis of TCGA data as well as direct assessment of patient primary specimens demonstrated that patient tumors with high HSF1 activity had lower numbers of CD8+ T cells. To functionally test this relationship, HSF1 was knocked down in 4T1 breast cancer cells and grown orthotopically in BALB/c mice. Tumors with HSF1 knockdown showed lower tumor volumes and increased CD8+ T cell infiltration. We further tested the effect of CD8+ T cells on the growth of HSF1 knockdown tumors by depleting CD8+ T cells in BALB/c mice. HSF1 knockdown tumors were significantly larger with CD8+ T cell depletion suggesting a functional role for HSF1 to inhibit CD8+ T cell infiltration and protect the tumor from immune-mediated killing. To investigate the mechanism by which HSF1 affects CD8+ T cells, we investigated whether HSF1 affects chemotactic cytokines. We found that loss of HSF1 significantly increased secretion of CCL5, a known chemoattractant for CD8+ T cells. Loss of HSF1 also increased mRNA levels of CCL5, suggesting a transcriptional effect on CCL5. To test the importance of CCL5 in the phenotype of HSF1 knockdown, a transwell migration assay was performed wherein T cells from BALB/c mice were placed in the upper chamber of a transwell chamber and the lower chamber contained conditioned medium from 4T1 cells with knockdown of HSF1 with or without knockdown of CCL5. The lower chamber was subjected to flow cytometry for CD3/CD8 to identify CD8+ T cells and we observed that loss of HSF1 increased migration of CD8+ T cells and this was ablated with additional loss of CCL5. These results suggest CCL5 is a significant mediator for the recruitment of CD8+ T cells when HSF1 is lost in cancer cells. We propose the model whereby high HSF1 activity in breast cancer cells suppresses expression and secretion of the chemo-attractant cytokine CCL5 that ultimately leads to a decrease in CD8+ T cells in breast tumors microenvironment. Citation Format: Curteisha LeeAnn Jacobs, Sakhi Shan, Wen-Cheng Lu, Richard Carpenter. HSF1 downregulation of CCL5 reduces CD8 + T cell trafficking in breast cancer [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2022; 2022 Apr 8-13. Philadelphia (PA): AACR; Cancer Res 2022;82(12_Suppl):Abstract nr 2192.
Abstract 5615: YH008, a PD-1-CD40 bispecific antibody, inhibits tumor growth in vivo through PD-1-dependent activation of CD40 signaling
Authors: Baihong Liu, Hao Yang, Li Hui, Benny Yang
Journal: Cancer Research (2022)

Abstract PD-1/PD-L1 inhibition immunotherapy is very popular in cancer treatment and has become one of the most pursued therapeutic strategies in the field. Combination treatment using anti-PD-1/PD-L1 agents with other immunomodulators brings additional benefits, such as preventing refractory effects towards PD-1/PD-L1 antibodies, and better inhibitory effects on tumor growth. Biocytogen developed YH008, a tetravalent anti PD-1/CD40 Fc-silenced IgG1 bispecific antibody (BsAb) that agonizes CD40 in a PD-1-dependent manner. Previously, YH008 demonstrated dose-dependent inhibitory efficacy against B16F10 engrafted tumors in PD-1/CD40 double humanized mice (established by Biocytogen: B-hPD1/CD40). Interestingly, in humanized CD40 mice that do not express human PD-1 expression, YH008 did not show tumor inhibition activity against the MC38 engrafted tumor. This observation indicates that YH008 activates the CD40 pathway in a PD-1 dependent manner. When compared with an anti-PD-L1/CD40 BsAb, YH008 showed superior tumor growth inhibition (TGI) against MC38 engrafted tumors in a triple humanized PD-1/PD-L1/CD40 mouse model (B-hPD-1/hPD-L1/hCD40). YH008 was observed to promote the proliferation and activation of dendritic cells, as well as increase CD8+/Treg ratio in B16F10 tumor-infiltrating lymphocytes (TILs). Furthermore, YH008 showed a superior liver toxicity profile compared to a selicrelumab analog. At a high dose of 100mg/kg, YH008 did not elevate liver enzymes in the blood of B-hPD1/hCD40 mice. Similarly, no significant adverse events were observed in a cynomolgus dose-escalation study. YH008 is currently in pre-clinical development with anticipated IND application in 2022. Citation Format: Baihong Liu, Hao Yang, Li Hui, Benny Yang. YH008, a PD-1-CD40 bispecific antibody, inhibits tumor growth in vivo through PD-1-dependent activation of CD40 signaling [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2022; 2022 Apr 8-13. Philadelphia (PA): AACR; Cancer Res 2022;82(12_Suppl):Abstract nr 5615.
Abstract 1474: Genome edited colorectal cancer organoid models reveal distinct microRNA activity patterns across different mutation profiles
Authors: Jonathan W. Villanueva, Lawrence Kwong, Teng Han, Salvador Alonso Martinez, Fong Cheng Pan, Michael T. Shanahan, Matt Kanke, Shuibing Chen, Lukas E. Dow, Charles G. Danko, Praveen Sethupathy
Journal: Cancer Research (2022)

Abstract Colorectal cancer (CRC) is the third most common cancer and second leading cause of cancer-related deaths worldwide. DNA mutations drive colon tumor formation by disrupting gene regulatory mechanisms that facilitate cell survival and growth. Distinct combinations of mutations can result in unique changes to these gene regulatory mechanisms leading to variability in responses to available therapeutics. MicroRNAs (miRNAs) are important regulators of gene expression in CRC and it is known that their expression can be altered by oncogenic mutations. However, it is unknown how distinct combinations of CRC-risk mutations differentially affect the regulation and expression of miRNAs. We hypothesize that some miRNAs will exhibit strong genotype-dependent changes in CRC whereas others will be altered irrespective of genotype. Utilizing sequencing data from The Cancer Genome Atlas (TCGA) and cutting-edge intestinal organoid (enteroid) models with different combinations of oncogenic mutations that commonly occur in CRC, we identified several distinct patterns of genotype-dependent miRNA expression. We also found a suite of miRNAs that are up-regulated in a mutation-independent manner. Among these, we demonstrated that miR-24-3p is a candidate master regulator of genes that are down-regulated in all mutational-contexts. RT-qPCR for miR-24-3p in genetically modified human colonoids with different combinations of oncogenic mutations further supports that miR-24-3p is elevated across various mutational contexts. Functional studies in the HCT116 cell line revealed that miR-24-3p controls the number of metabolically active, viable cells by regulating apoptosis but not proliferation. Moreover, follow-up ex vivo studies in mouse enteroids confirmed that miR-24 controls intestinal cell survival. To identify candidate gene targets that mediate the function of miR-24-3p, I performed an RNA-sequencing (RNA-seq) analysis and identified HMOX1 and PRSS8 as top candidate miR-24-3p targets. These findings suggest that miR-24-3p is a genotype-independent regulator of tumor cell apoptosis in CRC and merits further investigation. Overall, our findings provide a novel perspective on approaches for precision medicine in CRC. Citation Format: Jonathan W. Villanueva, Lawrence Kwong, Teng Han, Salvador Alonso Martinez, Fong Cheng Pan, Michael T. Shanahan, Matt Kanke, Shuibing Chen, Lukas E. Dow, Charles G. Danko, Praveen Sethupathy. Genome edited colorectal cancer organoid models reveal distinct microRNA activity patterns across different mutation profiles [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2022; 2022 Apr 8-13. Philadelphia (PA): AACR; Cancer Res 2022;82(12_Suppl):Abstract nr 1474.
Abstract 5983: Gene profile analysis of breast cancer lung metastasis, liver metastasis, brain metastasis and primary tumor
Authors: Yanman Fang, Hushan Zhang, Jiali Zou, Fulin Zhou, Xuejie Tang, Yi Yang, Li Luo, Yu Ding
Journal: Cancer Research (2022)

Abstract Background: The incidence of male breast cancer (MBC) is lower than female breast cancer (FBC), representing 1% of all breast cancer worldwide. The difference with FBC may affect the treatment strategy of MBC, but the necessary precondition is that we should know more about the difference between FBC and MBC. However, Because of its low incidence that the relevant data about MBC is relatively scarce. Here we report some data about gene mutation of MBC, and compared it with FBC. Methods: Blood or tumor Tissue samples of breast cancer were collected and subjected to NGS in a College of American Pathologists (CAP)-certified and Clinical Laboratory Improvement Amendments (CLIA)-accredited lab for gene mutation analysis (3D Medicines Inc.,Shanghai, China). Statistical analysis was performed using GraphPad Prism (version 7.01) and SPSS version 21.0 (SPSS,Inc.). Results: Approximately 182 samples were analyzed, among which, exist 82 samples were from primary tissue, 66 samples were breast cancer liver metastases, 20 were lung metastases and 14 were brain metastases. High genomic heterogeneity was found among primary breast cancer tissue, breast cancer liver metastases, lung metastases, brain metastases, that is at least 20 gene mutations were found in these BC samples, while different gene mutations were showed among primary and different metastases tissues. The top five mutated gene in primary tumor tissue were TP53(80.49%), PIK3CA(53.66%), FGF19(30.49%), ERBB2(26.83%), MYC(23.17%); in liver metastases tissues were TP53(54.55%), FGF19(39.39%), PIK3CA(37.88%), ERBB2(21.21%), CCND1(19.70%); in lung metastases tissues were TP53(70.00%), PIK3CA(55.00%), ERBB2,MCL1(25.00%), CDKN2A/2B(20.00%), CCND1, NF1, CDK12(15.00%), CCND2, MYC, PTEN, GNAS, FGF19, PTK2, FGFR1(10.00%); in brain metastases tissues were TP53(42.86%), PIK3CA(28.57%), ZNF703, PREX2, JAK3, MYC, FGFR1(14.29%). Besides, levels of TMB were also different among primary tissue, liver, lung and brain metastases tissues. Higher TMB level were showed in liver and brain metastases tissue than primary and lung metastases tissues (p&amp;lt;0.001). Conclusions: Different metastases of breast cancer were different in gene mutation landscape, this imply these patients should be managed differently. Citation Format: Yanman Fang, Hushan Zhang, Jiali Zou, Fulin Zhou, Xuejie Tang, Yi Yang, Li Luo, Yu Ding. Gene profile analysis of breast cancer lung metastasis, liver metastasis, brain metastasis and primary tumor [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2022; 2022 Apr 8-13. Philadelphia (PA): AACR; Cancer Res 2022;82(12_Suppl):Abstract nr 5983.